After Colony 195, December 24th, Christmas Eve, The universe saw the greatest battle between humans, as World Nation (Earth) and White Fang (Space Colonists) were locked in a bloody battle. The Gundam Pilots finally ended this conflict, while the leader of World Nation Treize Khushrenada was killed and White Fang's leader Milliardo Peacecraft disappeared. Having seen the violence, terror and hatred of war, the people on Earth and the space colonies put prejudice aside and strive for peace. And thus a new world government is established The Earth Sphere Unified Nation.

The year is AC (After Colony) 196, one year after the war between the Earth and the colonies, and now the Earth and the colonies have chose to co-exist with each other. Under this new government, Earth and Space began a series of disarmaments and in the short space of a year; all mobile suits have been destroyed. Since Gundams are no longer needed in a time of peace, the Gundam pilots Heero Yuy, Duo Maxwell, Trowa Barton and Quatre Raberba Winner decided to farewell their Gundams by sending them into the sun. However, as long as mankind exists, there will always be battles.

Relena Darlian, now the deputy foreign minister for the new government is abducted during a visit to the colony X-18999. The person behind this scheme was a little girl named Mariemaia Khushrenada, heir to the mysterious Barton Foundation, and daughter of former World Nation leader, Treize Khushrenada. Mariemaia is determined to follow her father's footsteps and conquer the world, while the former Queen Relena will be a great propaganda tool.

While on a visit to X-18999 will the circus, Trowa stubbles across the Barton Foundation and began investigation. Similarly Heero and Duo realized Relena had been abducted and also set out to investigate. With former allies, Sally Po and Lucrezia Noin, now government agents (Preventer), the pilots began to sneak into X-18999.

The pilots soon realized that the colony was a huge Mobile Suit and weapons factory, and this was soon followed by Mariemaia's declaration of war on the Earth. Her grandfather, Dekim Barton, was the planner of the scheme. Trowa tried to assassinate Dekim, but the fifth Gundam Pilot, Chang Wufei, stopped him. Meanwhile, both Heero and Duo were able to infiltrate the base, but only to be stopped by Wufei, and Trowa as well. All seems lost, as Mariemaia mobilized her army and began her invasion of Earth. At the same time, a mysterious blond-haired man approaches Lady Une at the Preventer Headquarters it's the Lightning Count (Milliardo Peacecraft).

As Dekim launches his attack, a lone Mobile Suit appears, the Tallgeese III, piloted by Milliardo Peacecraft began attacking Dekim's legions of MS's. Dekim counters are threatening to drop space colonies onto the Earth, and reluctantly Milliardo gave in. By now Heero, Duo and Trowa was able to escape from X-18999 while Quatre was able to retrieves the Gundams.

Since Earth is now disarmed, Mariemaia's invasion was swift and easy, she quickly seized control of the government's headquarters at Brussels and retreats to a fortified bunker. The only ones fighting against her huge legions of mobile suits were Milliardo's in his Tallgeese III and Noin in her White Taurus. Back in space, the Gundam team reunites, and Duo in his Deathscythe Hell, Quatre in his Sandrock and Trowa in his Heavyarms head straight back to Earth, joining Milliardo and Noin's fight against Mariemaia. Now, Heero in his Wing Zero is locked in battle with Wufei's Altron. The two fought a spectacular fight until Heero, tired of the endless fighting, breaks off the fight and plunges into the sea.

The battle continues, but Duo, Trowa, Quatre, Milliardo and Noin are seriously outnumbered, just as all seems lost, a battered Wing Zero suddenly appears in the sky, with the Twin-Buster Rifle pointing at the fortified bunker. Heero repeatedly fires at the bunker until all its barriers and Wing Zero are destroyed, while Wufei has rejoined his comrades. Mariemaia finally realizes her mistake, and began to surrender, however, Dekim refused and shots at Relena. Mariemaia pushes Relena out of the way and took the bullet herself, while Dekim in disbelief; he was shot by one of his own underlings. Heero suddenly arrives; ready to finish his mission by killing Mariemaia, only to discover that his gun was empty. The perfect soldier signs that he doesn't need to kill anyone anymore, and passes out.

With Mariemaia step down, the conflict ended. All the weapons and uniformed was destroyed. While, all the Gundam Pilots self-destructed their own Gundams. Peace was finally achieved on that day.

Lady Une and the recovering Mariemaia visit her father's grave, Duo and his friend Hilde happily returns to their salvage business, Wufei and Sally now works for The Preventer, Milliardo and Noin went off to space for a secret mission, Trowa went back working with Catherine in the circus, Quatre using his wealth started rebuilding the space colonies, while Relena continues her work as a diplomat between the Earth and the colonies. And finally, Heero slowly disappear into a crowd of people and never seen again.